# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 23:17:15 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 5'-deoxy-5'-[({6-[(alpha-D-galactopyranosyloxy)methyl]pyridin-2-yl}carbonyl)amino]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](OCc2cccc(n2)C(=O)NC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O)[C@H](O)[C@@H](O)[C@H]1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 WS3  WS3  5'-deoxy-5'-[({6-[(alpha-D-galactopyranosyloxy)methyl]pyridin-2-yl}carbonyl)amino]uridine  ligand  66  38  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WS3
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 WS3  O4   O  O     0  -0.465  -5.6098   4.6120  -0.1582
 WS3  C4   C  CR6   0   0.567  -5.2209   3.5163   0.2019
 WS3  N3   N  NR16  0  -0.731  -5.4762   3.0650   1.4887
 WS3  C2   C  CR6   0   0.740  -5.1158   1.8681   2.0448
 WS3  O2   O  O     0  -0.479  -5.3877   1.5713   3.1904
 WS3  C5   C  CR16  0  -0.507  -4.4772   2.5738  -0.5943
 WS3  C6   C  CR16  0   0.089  -4.1137   1.3925  -0.0659
 WS3  N1   N  NR6   0  -0.569  -4.4225   1.0194   1.2072
 WS3  C11  C  CR15  0   0.188  -4.0188  -0.2824   1.7861
 WS3  O44  O  O     0  -0.499  -3.0578  -0.8800   0.9742
 WS3  C22  C  CR15  0  -0.040  -5.1990  -1.2525   1.8667
 WS3  O22  O  OH1   0  -0.664  -4.9674  -2.1100   2.9498
 WS3  C33  C  CR15  0  -0.037  -5.0629  -1.9981   0.5344
 WS3  O33  O  OH1   0  -0.655  -5.6165  -3.2827   0.5413
 WS3  C44  C  CR15  0   0.032  -3.5496  -2.0806   0.3765
 WS3  C55  C  CH2   0  -0.316  -3.0910  -2.1736  -1.0656
 WS3  N11  N  NH1   0  -0.646  -1.6590  -2.2040  -1.2010
 WS3  C12  C  C     0   0.535  -0.9491  -3.3244  -1.3816
 WS3  O13  O  O     0  -0.479  -1.4307  -4.4446  -1.4701
 WS3  C14  C  CR6   0   0.114   0.5343  -3.1034  -1.4878
 WS3  C15  C  CR16  0  -0.303   1.3737  -4.1710  -1.7648
 WS3  C16  C  CR16  0  -0.140   2.7332  -3.9146  -1.8597
 WS3  C17  C  CR16  0  -0.328   3.1992  -2.6247  -1.6687
 WS3  C18  C  CR6   0   0.194   2.2767  -1.6210  -1.3844
 WS3  N19  N  N     0  -0.465   0.9774  -1.8665  -1.3015
 WS3  C20  C  CH2   0  -0.175   2.6837  -0.1895  -1.1698
 WS3  O1'  O  O2    0  -0.494   4.0682  -0.1389  -0.9575
 WS3  C1'  C  CH1   0   0.256   4.6670   1.0996  -1.1556
 WS3  O5'  O  O2    0  -0.501   4.2697   2.0439  -0.2058
 WS3  C5'  C  CH1   0  -0.014   4.6169   1.7212   1.1333
 WS3  C6'  C  CH2   0  -0.159   4.0558   2.8036   2.0303
 WS3  O6'  O  OH1   0  -0.669   2.6499   2.7347   1.9871
 WS3  C4'  C  CH1   0  -0.006   6.1217   1.5552   1.2930
 WS3  O4'  O  OH1   0  -0.674   6.7453   2.8010   1.0949
 WS3  C3'  C  CH1   0   0.004   6.6205   0.5127   0.2944
 WS3  O3'  O  OH1   0  -0.677   8.0228   0.4481   0.4088
 WS3  C2'  C  CH1   0  -0.019   6.1844   0.8979  -1.1139
 WS3  O2'  O  OH1   0  -0.666   6.6153  -0.1094  -1.9950
 WS3  H1   H  HNR6  0   0.427  -5.9954   3.6855   2.0982
 WS3  H2   H  HCR6  0   0.292  -4.2066   2.8239  -1.6082
 WS3  H3   H  HCR6  0   0.324  -3.5371   0.6883  -0.6438
 WS3  H4   H  HCR5  0   0.289  -3.5991  -0.0753   2.7723
 WS3  H5   H  HCR5  0   0.262  -6.1605  -0.7343   1.9540
 WS3  H6   H  HOH1  0   0.452  -5.3711  -2.9620   2.7428
 WS3  H7   H  HCR5  0   0.247  -5.4893  -1.3820  -0.2694
 WS3  H8   H  HOH1  0   0.470  -6.5586  -3.2175   0.3542
 WS3  H9   H  HCR5  0   0.256  -3.1634  -2.9420   0.9341
 WS3  H10  H  HCH2  0   0.274  -3.5113  -3.0800  -1.5017
 WS3  H11  H  HCH2  0   0.260  -3.4820  -1.3322  -1.6423
 WS3  H12  H  HNH1  0   0.407  -1.1379  -1.3427  -1.1226
 WS3  H13  H  HCR6  0   0.274   0.9784  -5.1665  -1.9052
 WS3  H14  H  HCR6  0   0.279   3.4255  -4.7163  -2.0799
 WS3  H15  H  HCR6  0   0.276   4.2537  -2.3999  -1.7404
 WS3  H16  H  HCH2  0   0.240   2.3967   0.3976  -2.0539
 WS3  H17  H  HCH2  0   0.241   2.1205   0.2181  -0.3225
 WS3  H18  H  HCH1  0   0.239   4.3640   1.5201  -2.1252
 WS3  H19  H  HCH1  0   0.235   4.1560   0.7686   1.4283
 WS3  H20  H  HCH2  0   0.200   4.4386   2.6315   3.0451
 WS3  H21  H  HCH2  0   0.207   4.4243   3.7839   1.7085
 WS3  H22  H  HOH1  0   0.456   2.3009   3.4788   2.4857
 WS3  H23  H  HCH1  0   0.234   6.3083   1.1790   2.3104
 WS3  H24  H  HOH1  0   0.451   7.6966   2.6517   1.0602
 WS3  H25  H  HCH1  0   0.221   6.1660  -0.4531   0.5568
 WS3  H26  H  HOH1  0   0.454   8.3669  -0.0427  -0.3455
 WS3  H27  H  HCH1  0   0.233   6.6409   1.8629  -1.3673
 WS3  H28  H  HOH1  0   0.460   6.6570   0.2520  -2.8854

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 WS3  O22  C22  single    1.401  0.020  1.401
 WS3  O33  C33  single    1.399  0.020  1.399
 WS3  C22  C33  single    1.533  0.020  1.533
 WS3  C22  C11  single    1.530  0.020  1.530
 WS3  C33  C44  single    1.524  0.020  1.524
 WS3  C44  C55  single    1.516  0.020  1.516
 WS3  C44  O44  single    1.429  0.020  1.429
 WS3  O6'  C6'  single    1.408  0.020  1.408
 WS3  O13  C12  double    1.223  0.020  1.223
 WS3  C55  N11  single    1.439  0.020  1.439
 WS3  C6'  C5'  single    1.514  0.020  1.514
 WS3  O44  C11  single    1.393  0.020  1.393
 WS3  C11  N1   single    1.481  0.020  1.481
 WS3  C12  N11  single    1.339  0.020  1.339
 WS3  C12  C14  single    1.504  0.020  1.504
 WS3  O2   C2   double    1.214  0.020  1.214
 WS3  C5'  O5'  single    1.421  0.020  1.421
 WS3  C5'  C4'  single    1.522  0.020  1.522
 WS3  N1   C2   single    1.379  0.020  1.379
 WS3  N1   C6   single    1.362  0.020  1.362
 WS3  C2   N3   single    1.368  0.020  1.368
 WS3  O5'  C1'  single    1.397  0.020  1.397
 WS3  N19  C14  aromatic  1.327  0.020  1.327
 WS3  N19  C18  aromatic  1.325  0.020  1.325
 WS3  C14  C15  aromatic  1.386  0.020  1.386
 WS3  O4'  C4'  single    1.407  0.020  1.407
 WS3  C4'  C3'  single    1.527  0.020  1.527
 WS3  C6   C5   double    1.344  0.020  1.344
 WS3  C20  C18  single    1.504  0.020  1.504
 WS3  C20  O1'  single    1.402  0.020  1.402
 WS3  C18  C17  aromatic  1.393  0.020  1.393
 WS3  N3   C4   single    1.387  0.020  1.387
 WS3  C1'  O1'  single    1.390  0.020  1.390
 WS3  C1'  C2'  single    1.531  0.020  1.531
 WS3  C15  C16  aromatic  1.387  0.020  1.387
 WS3  C3'  C2'  single    1.524  0.020  1.524
 WS3  C3'  O3'  single    1.408  0.020  1.408
 WS3  C5   C4   single    1.441  0.020  1.441
 WS3  C4   O4   double    1.217  0.020  1.217
 WS3  C2'  O2'  single    1.406  0.020  1.406
 WS3  C17  C16  aromatic  1.385  0.020  1.385
 WS3  N3   H1   single    0.860  0.020  1.020
 WS3  C5   H2   single    0.930  0.020  1.080
 WS3  C6   H3   single    0.930  0.020  1.080
 WS3  C11  H4   single    0.970  0.020  1.090
 WS3  C22  H5   single    0.970  0.020  1.090
 WS3  O22  H6   single    0.850  0.020  0.980
 WS3  C33  H7   single    0.970  0.020  1.090
 WS3  O33  H8   single    0.850  0.020  0.980
 WS3  C44  H9   single    0.970  0.020  1.090
 WS3  C55  H10  single    0.970  0.020  1.090
 WS3  C55  H11  single    0.970  0.020  1.090
 WS3  N11  H12  single    0.860  0.020  1.020
 WS3  C15  H13  single    0.930  0.020  1.080
 WS3  C16  H14  single    0.930  0.020  1.080
 WS3  C17  H15  single    0.930  0.020  1.080
 WS3  C20  H16  single    0.970  0.020  1.090
 WS3  C20  H17  single    0.970  0.020  1.090
 WS3  C1'  H18  single    0.970  0.020  1.090
 WS3  C5'  H19  single    0.970  0.020  1.090
 WS3  C6'  H20  single    0.970  0.020  1.090
 WS3  C6'  H21  single    0.970  0.020  1.090
 WS3  O6'  H22  single    0.850  0.020  0.980
 WS3  C4'  H23  single    0.970  0.020  1.090
 WS3  O4'  H24  single    0.850  0.020  0.980
 WS3  C3'  H25  single    0.970  0.020  1.090
 WS3  O3'  H26  single    0.850  0.020  0.980
 WS3  C2'  H27  single    0.970  0.020  1.090
 WS3  O2'  H28  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 WS3  C5   C4   N3   113.26  3.000
 WS3  C5   C4   O4   126.18  3.000
 WS3  N3   C4   O4   120.56  3.000
 WS3  H1   N3   C2   115.24  3.000
 WS3  H1   N3   C4   116.95  3.000
 WS3  C2   N3   C4   127.82  3.000
 WS3  N1   C2   O2   122.35  3.000
 WS3  N1   C2   N3   115.08  3.000
 WS3  O2   C2   N3   122.57  3.000
 WS3  H2   C5   C6   120.35  3.000
 WS3  H2   C5   C4   119.82  3.000
 WS3  C6   C5   C4   119.82  3.000
 WS3  H3   C6   N1   116.31  3.000
 WS3  H3   C6   C5   120.53  3.000
 WS3  N1   C6   C5   123.15  3.000
 WS3  C11  N1   C6   122.99  3.000
 WS3  C6   N1   C2   120.86  3.000
 WS3  C11  N1   C2   116.14  3.000
 WS3  H4   C11  C22  111.67  3.000
 WS3  H4   C11  O44  110.04  3.000
 WS3  C22  C11  O44  106.91  3.000
 WS3  H4   C11  N1   106.93  3.000
 WS3  O44  C11  N1   109.72  3.000
 WS3  C22  C11  N1   111.58  3.000
 WS3  C44  O44  C11  111.53  3.000
 WS3  H5   C22  C33  112.16  3.000
 WS3  H5   C22  O22  111.90  3.000
 WS3  C33  C22  O22  111.08  3.000
 WS3  H5   C22  C11  112.41  3.000
 WS3  C33  C22  C11  101.20  3.000
 WS3  O22  C22  C11  107.54  3.000
 WS3  H6   O22  C22  107.78  3.000
 WS3  H7   C33  C44  109.88  3.000
 WS3  H7   C33  O33  111.40  3.000
 WS3  C44  C33  O33  110.12  3.000
 WS3  H7   C33  C22  109.18  3.000
 WS3  C44  C33  C22  101.80  3.000
 WS3  O33  C33  C22  114.03  3.000
 WS3  H8   O33  C33  108.92  3.000
 WS3  H9   C44  C55  109.20  3.000
 WS3  H9   C44  C33  109.86  3.000
 WS3  C55  C44  C33  113.72  3.000
 WS3  H9   C44  O44  109.04  3.000
 WS3  C55  C44  O44  110.21  3.000
 WS3  C33  C44  O44  104.66  3.000
 WS3  H11  C55  H10  106.93  3.000
 WS3  H11  C55  N11  108.83  3.000
 WS3  H10  C55  N11  109.18  3.000
 WS3  H11  C55  C44  110.28  3.000
 WS3  H10  C55  C44  108.36  3.000
 WS3  N11  C55  C44  113.07  3.000
 WS3  H12  N11  C12  116.79  3.000
 WS3  H12  N11  C55  119.23  3.000
 WS3  C12  N11  C55  123.94  3.000
 WS3  C14  C12  O13  121.21  3.000
 WS3  C14  C12  N11  114.19  3.000
 WS3  O13  C12  N11  124.59  3.000
 WS3  N19  C14  C15  122.94  3.000
 WS3  C15  C14  C12  119.89  3.000
 WS3  N19  C14  C12  117.16  3.000
 WS3  H13  C15  C16  121.35  3.000
 WS3  H13  C15  C14  120.94  3.000
 WS3  C16  C15  C14  117.71  3.000
 WS3  H14  C16  C17  120.20  3.000
 WS3  H14  C16  C15  120.28  3.000
 WS3  C17  C16  C15  119.52  3.000
 WS3  H15  C17  C18  120.66  3.000
 WS3  H15  C17  C16  120.87  3.000
 WS3  C18  C17  C16  118.46  3.000
 WS3  C20  C18  N19  115.65  3.000
 WS3  C20  C18  C17  122.41  3.000
 WS3  N19  C18  C17  121.93  3.000
 WS3  C18  N19  C14  119.43  3.000
 WS3  H17  C20  H16  106.79  3.000
 WS3  H17  C20  O1'  112.15  3.000
 WS3  H16  C20  O1'  111.12  3.000
 WS3  H17  C20  C18  108.99  3.000
 WS3  H16  C20  C18  108.84  3.000
 WS3  O1'  C20  C18  108.87  3.000
 WS3  C1'  O1'  C20  115.86  3.000
 WS3  H18  C1'  C2'  110.33  3.000
 WS3  H18  C1'  O5'  105.23  3.000
 WS3  C2'  C1'  O5'  110.63  3.000
 WS3  H18  C1'  O1'  110.35  3.000
 WS3  C2'  C1'  O1'  107.79  3.000
 WS3  O5'  C1'  O1'  112.51  3.000
 WS3  C5'  O5'  C1'  114.70  3.000
 WS3  H19  C5'  C4'  106.98  3.000
 WS3  H19  C5'  C6'  107.79  3.000
 WS3  C4'  C5'  C6'  112.47  3.000
 WS3  H19  C5'  O5'  110.33  3.000
 WS3  C4'  C5'  O5'  111.43  3.000
 WS3  C6'  C5'  O5'  107.79  3.000
 WS3  H21  C6'  H20  107.12  3.000
 WS3  H21  C6'  O6'  111.75  3.000
 WS3  H20  C6'  O6'  111.63  3.000
 WS3  H21  C6'  C5'  109.95  3.000
 WS3  H20  C6'  C5'  107.84  3.000
 WS3  O6'  C6'  C5'  108.48  3.000
 WS3  H22  O6'  C6'  107.98  3.000
 WS3  H23  C4'  C3'  108.41  3.000
 WS3  H23  C4'  O4'  110.95  3.000
 WS3  C3'  C4'  O4'  111.57  3.000
 WS3  H23  C4'  C5'  107.56  3.000
 WS3  C3'  C4'  C5'  109.19  3.000
 WS3  O4'  C4'  C5'  109.07  3.000
 WS3  H24  O4'  C4'  107.78  3.000
 WS3  H25  C3'  C2'  108.93  3.000
 WS3  H25  C3'  O3'  110.62  3.000
 WS3  C2'  C3'  O3'  111.82  3.000
 WS3  H25  C3'  C4'  107.97  3.000
 WS3  O3'  C3'  C4'  107.66  3.000
 WS3  C2'  C3'  C4'  109.77  3.000
 WS3  H26  O3'  C3'  108.38  3.000
 WS3  H27  C2'  O2'  110.97  3.000
 WS3  H27  C2'  C3'  108.46  3.000
 WS3  O2'  C2'  C3'  108.08  3.000
 WS3  H27  C2'  C1'  106.86  3.000
 WS3  O2'  C2'  C1'  112.40  3.000
 WS3  C3'  C2'  C1'  110.01  3.000
 WS3  H28  O2'  C2'  108.91  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 WS3  CONST_01  C17  C18  N19  C14    0.00   0.0  0
 WS3  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 WS3  CONST_03  C18  N19  C14  C15    0.00   0.0  0
 WS3  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 WS3  CONST_05  N19  C14  C15  C16    0.00   0.0  0
 WS3  CONST_06  N19  C18  C17  C16    0.00   0.0  0
 WS3  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 WS3  CONST_08  C11  N1   C2   N3   180.00   0.0  0
 WS3  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 WS3  CONST_10  C5   C4   N3   C2     0.00   0.0  0
 WS3  CONST_11  C18  N19  C14  C12  180.00   0.0  0
 WS3  CONST_12  C16  C15  C14  C12  180.00   0.0  0
 WS3  CONST_13  C20  C18  N19  C14  180.00   0.0  0
 WS3  CONST_14  C20  C18  C17  C16  180.00   0.0  0
 WS3  CONST_15  C2   N3   C4   O4   180.00   0.0  0
 WS3  CONST_16  O2   C2   N3   C4   180.00   0.0  0
 WS3  CONST_17  C11  N1   C2   O2     0.00   0.0  0
 WS3  CONST_18  C6   N1   C2   O2   180.00   0.0  0
 WS3  CONST_19  H14  C16  C15  C14  180.00   0.0  0
 WS3  CONST_20  H15  C17  C16  C15  180.00   0.0  0
 WS3  CONST_21  H13  C15  C16  C17  180.00   0.0  0
 WS3  CONST_22  H1   N3   C4   C5   180.00   0.0  0
 WS3  CONST_23  C14  C12  N11  C55  180.00   0.0  0
 WS3  CONST_24  H12  N11  C12  C14    0.00   0.0  0
 WS3  CONST_25  O13  C12  N11  C55    0.00   0.0  0
 WS3  Var_01    N19  C14  C12  N11    4.53  30.0  2
 WS3  Var_02    O1'  C20  C18  C17  -15.24  30.0  1
 WS3  Var_03    C12  N11  C55  C44   99.15  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 WS3  chir_01  C11  C22  O44  N1   negativ
 WS3  chir_02  C22  O22  C11  C33  negativ
 WS3  chir_03  C33  O33  C22  C44  negativ
 WS3  chir_04  C44  O44  C33  C55  negativ
 WS3  chir_05  C1'  O5'  O1'  C2'  positiv
 WS3  chir_06  C5'  O5'  C6'  C4'  positiv
 WS3  chir_07  C4'  O4'  C5'  C3'  negativ
 WS3  chir_08  C3'  O3'  C2'  C4'  positiv
 WS3  chir_09  C2'  O2'  C3'  C1'  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 WS3  plan-1  O4   0.020
 WS3  plan-1  C4   0.020
 WS3  plan-1  N3   0.020
 WS3  plan-1  C2   0.020
 WS3  plan-1  O2   0.020
 WS3  plan-1  C5   0.020
 WS3  plan-1  C6   0.020
 WS3  plan-1  N1   0.020
 WS3  plan-1  C11  0.020
 WS3  plan-1  H1   0.020
 WS3  plan-1  H2   0.020
 WS3  plan-1  H3   0.020
 WS3  plan-2  C12  0.020
 WS3  plan-2  C14  0.020
 WS3  plan-2  C15  0.020
 WS3  plan-2  C16  0.020
 WS3  plan-2  C17  0.020
 WS3  plan-2  C18  0.020
 WS3  plan-2  N19  0.020
 WS3  plan-2  C20  0.020
 WS3  plan-2  H13  0.020
 WS3  plan-2  H14  0.020
 WS3  plan-2  H15  0.020
 WS3  plan-3  C55  0.020
 WS3  plan-3  N11  0.020
 WS3  plan-3  C12  0.020
 WS3  plan-3  O13  0.020
 WS3  plan-3  C14  0.020
 WS3  plan-3  H12  0.020

